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  "Package": "glinvci",
  "Type": "Package",
  "Title": "Phylogenetic Comparative Methods with Uncertainty Estimates",
  "Version": "1.2.4",
  "Date": "2024-04-16",
  "Authors@R": "c(person(family=\"Kiang\", given=\"Woodrow\", role=c(\"cre\",\"aut\"), email=\"hello@hckiang.com\"))",
  "Maintainer": "Woodrow Kiang <hello@hckiang.com>",
  "Description": "A framework for analytically computing the asymptotic\nconfidence intervals and maximum-likelihood estimates of a\nclass of continuous-time Gaussian branching processes defined\nby Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019)\n<doi:10.1016/j.tpb.2019.11.005>. The class of model includes\nthe widely used Ornstein-Uhlenbeck and Brownian motion\nbranching processes. The framework is designed to be flexible\nenough so that the users can easily specify their own\nsub-models, or re-parameterizations, and obtain the\nmaximum-likelihood estimates and confidence intervals of their\nown custom models.",
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    "dou_symH_fixedtheta_fixedSig",
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    "get_restricted_ou",
    "glinv",
    "glinv_gauss",
    "grad",
    "has_tipvals",
    "hbrn",
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    "hbrn_fixedSig",
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    "nparams_ou_symH_fixedSig",
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    "nparams_ou_symH_fixedtheta_diagSig",
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    "ou_diagH_fixedtheta_fixedSig",
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    "oupar",
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    "set_tips",
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        "clone_model.glinv_gauss"
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    {
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      "topics": [
        "fit.glinv"
      ]
    },
    {
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      "topics": [
        "get_restricted_ou"
      ]
    },
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      "title": "Construct an GLInv model with respect to user-specified parametrisation",
      "topics": [
        "glinv",
        "grad.glinv",
        "hess.glinv",
        "lik.glinv",
        "plot.glinv",
        "print.glinv"
      ]
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    {
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      "title": "Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters.",
      "topics": [
        "glinv_gauss",
        "grad.glinv_gauss",
        "hess.glinv_gauss",
        "lik.glinv_gauss",
        "print.glinv_gauss"
      ]
    },
    {
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      "title": "glinvci: Confidence intervals and hypothesis testing for GLInv model",
      "topics": [
        "glinvci-package",
        "glinvci"
      ]
    },
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    },
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        "has_tipvals",
        "has_tipvals.glinv",
        "has_tipvals.glinv_gauss"
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    },
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      "title": "Compute the log-likelihood Hessian of GLInv models",
      "topics": [
        "hess"
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    },
    {
      "page": "lik",
      "title": "Compute the likelihood of a GLInv model",
      "topics": [
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    {
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      "title": "Getting marginal confidence interval for GLInv model",
      "topics": [
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    {
      "page": "nparams_ou",
      "title": "Get the number of parameters of the unrestricted OU model",
      "topics": [
        "nparams_ou"
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    },
    {
      "page": "ou_haltlost",
      "title": "Handling missing data and lost traits in Ornstein-Uhlenbeck processes",
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